Evidence on the prevalence of lower back pain (LBP) among nurses is widespread in the literature, with several risk factors being reported. These include manual handling of patients, repetitive bending and twisting movements, and long working hours. It is reported that LBP has negative health outcomes and causes poor work performance among healthcare workers (HCWs). The magnitude of ergonomic risks associated with these healthcare activities has not been adequately investigated in Botswana. Thus, this study aimed to investigate the ergonomic risk levels associated with the manual handling of patients and its association with the prevalence of LBP among nurses in Botswana. This was an observational cross-sectional hospital-based study conducted in a Botswana public tertiary hospital from March to April 2023. The Movement and Assistance of Hospital Patients (MAPO) tool was used to collect data on ergonomic risk levels. Data on the demographic characteristics of participants were collected using a tool adapted from the Nordic Musculoskeletal Questionnaire (NMQ). Odds ratios and 95% confidence intervals were estimated to determine the association between ergonomic risk levels and the prevalence of LBP. A total of 256 nurses participated and completed the study. The self-reported prevalence of LBP in this study was 76.6%. The risk of acquiring LBP was high (90.5%) based on the MAPO index. Although the frequencies of self-reported LBP were high among nurses, these did not show any significant association with the MAPO index data. This could be partly due to the small sample size. There was a high prevalence of LBP in this study, which was corroborated by the MAPO index data. This has demonstrated the value of the MAPO index in forecasting the risk of patient manual handling. The findings might help Botswana formulate policies intended to address ergonomic preventive measures, directed towards reducing the MAPO index score by addressing the single risk determinants.